Postprocessing of protein-ligand docking poses using linear response MM-PB/SA: Application to Wee1 kinase inhibitors

Journal of Chemical Information and Modeling

Volumn 50, Issue 9, 2010, Pages 1574-1588

  Wichapong, Kanin ^a,b   Lawson, Michael ^b   Pianwanit, Somsak ^a   Kokpol, Sirirat ^a   Sippl, Wolfgang ^b  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; DIGITAL LIBRARIES; ENZYME INHIBITION; FREE ENERGY; LIGANDS;

BINDING FREE ENERGY; BIOLOGICAL AFFINITY; COMPOUND LIBRARIES; INTERACTION ENERGIES; KINASE INHIBITORS; PROTEIN FLEXIBILITY; PROTEIN-LIGAND DOCKING; STRUCTURE BASED DRUG DESIGNS;

BINDING ENERGY;

CELL CYCLE PROTEIN; LIGAND; NUCLEAR PROTEIN; PROTEIN KINASE INHIBITOR; PROTEIN TYROSINE KINASE; WEE1 PROTEIN, HUMAN;

ARTICLE; CHEMICAL STRUCTURE; DRUG ANTAGONISM; DRUG DESIGN; PROTEIN BINDING; PROTEIN PROCESSING; STATIC ELECTRICITY;

CELL CYCLE PROTEINS; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; NUCLEAR PROTEINS; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN-TYROSINE KINASES; STATIC ELECTRICITY;

EID: 77957242467     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci1002153     Document Type: Article

References (45)

1. Klebe, G. Virtual ligand screening: strategies, perspectives and limitations Drug Discovery Today 2006, 11, 580-594 (Pubitemid 43912502)
2. Aqvist, J.; Marelius, J. The linear interaction energy method for predicting ligand binding free energies Comb. Chem. High Throughput Screening 2001, 4, 613-626 (Pubitemid 34003156)
3. Carlsson, J.; Boukharta, L.; Aqvist, J. Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase J. Med. Chem. 2008, 51, 2648-2656 (Pubitemid 351620786)
4. Aqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drug design Protein Eng. 1994, 7, 385-391 (Pubitemid 24063137)
5. Stjernschantz, E.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N. P.; Oostenbrink, C. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method J. Chem. Inf. Model. 2006, 46, 1972-1983 (Pubitemid 44625969)
6. van Lipzig, M. M.; ter Laak, A. M.; Jongejan, A.; Vermeulen, N. P.; Wamelink, M.; Geerke, D.; Meerman, J. H. Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method J. Med. Chem. 2004, 12, 1018-1030 (Pubitemid 38176805)
7. Jones-Hertzog, D. K.; Jorgensen, W. L. Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method J. Med. Chem. 1997, 40, 1539-1549
8. Huang, D.; Caflisch, A. Efficient evaluation of binding free energy using continuum electrostatics solvation J. Med. Chem. 2004, 47, 5791-5797 (Pubitemid 39447274)
9. Warwicker, J.; Watson, H. C. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles J. Mol. Biol. 1982, 157, 671-679
10. Kolb, P.; Huang, D.; Dey, F.; Caflisch, A. Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model J. Med. Chem. 2008, 51, 1179-1188 (Pubitemid 351480380)
11. Ekonomiuk, D.; Su, X. C.; Ozawa, K.; Bodenreider, C.; Lim, S. P.; Yin, Z.; Keller, T. H.; Beer, D.; Patel, V.; Otting, G.; Caflisch, A.; Huang, D. Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking PLoS Negl. Trop. Dis. 2009, 3 e356
12. Huang, D.; Lüthi, U.; Kolb, P.; Cecchini, M.; Barberis, A.; Caflisch, A. In silico discovery of beta-secretase inhibitors J. Am. Chem. Soc. 2006, 128, 5436-5443
13. Huang, D.; Lüthi, U.; Kolb, P.; Edler, K.; Cecchini, M.; Audetat, S.; Barberis, A.; Caflisch, A. Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations J. Med. Chem. 2005, 48, 5108-5111 (Pubitemid 41113898)
14. Zhou, Z.; Madura, J. D. Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS Proteins 2004, 57, 493-503 (Pubitemid 39390804)
15. Zhou, Z.; Bates, M.; Madura, J. D. Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design Proteins 2006, 65, 580-592 (Pubitemid 44583209)
16. Zhou, Z.; Wang, Y.; Bryant, S. H. Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex J. Comput. Chem. 2009, 30, 2165-2175
17. Palmer, B. D.; Smaill, J. B.; Rewcastle, G. W.; Dobrusin, E. M.; Kraker, A.; Moore, C. W.; Steinkampf, R. W.; Denny, W. A. Structure-activity relationships for 2-anilino-6-phenylpyrido[2,3-d]pyrimidin-7(8H)-ones as inhibitors of the cellular checkpoint kinase Wee1 Bioorg. Med. Chem. Lett. 2005, 15, 1931-1935 (Pubitemid 40380762)
18. Palmer, B. D.; Thompson, A. M.; Booth, R. J.; Dobrusin, E. M.; Kraker, A. J.; Lee, H. H.; Lunney, E. A.; Mitchell, L. H.; Ortwine, D. F.; Smaill, J. B.; Swan, L. M.; Denny, W. A. 4-Phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione inhibitors of the checkpoint kinase Wee1. Structure-activity relationships for chromophore modification and phenyl ring substitution J. Med. Chem. 2006, 49, 4896-4911
19. Smaill, J. B.; Baker, E. N.; Booth, R. J.; Bridges, A. J.; Dickson, J. M.; Dobrusin, E. M.; Ivanovic, I.; Kraker, A. J.; Lee, H. H.; Lunney, E. A.; Ortwine, D. F.; Palmer, B. D.; Quin, J., III.; Squire, C. J.; Thompson, A. M.; Denny, W. A. Synthesis and structure-activity relationships of N-6 substituted analogues of 9-hydroxy-4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones as inhibitors of Wee1 and Chk1 checkpoint kinases Eur. J. Med. Chem. 2008, 43, 1276-1296 (Pubitemid 351734546)
20. Smaill, J. B.; Lee, H. H.; Palmer, B. D.; Thompson, A. M.; Squire, C. J.; Baker, E. N.; Booth, R. J.; Kraker, A.; Hook, K.; Denny, W. A. Synthesis and structure-activity relationships of soluble 8-substituted 4-(2-chlorophenyl)-9- hydroxypyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones as inhibitors of the Wee1 and Chk1 checkpoint kinases Bioorg. Med. Chem. Lett. 2008, 18, 929-933 (Pubitemid 351179362)
21. Sybyl7.2, Tripos Inc.: South Hanley, St. Louis, MO, 2007.
22. Halgren, T. A. Merck Molecular Force Field: I. Basis, Form, Scope, Parameterization and Performance of MMFF94 J. Comput. Chem. 1996, 17, 490-519
23. Halgren, T. A. Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions J. Comput. Chem. 1996, 17, 520-552
24. Halgren, T. A. Merck Molecular Force Field. III. Molecular Geometries and Vibrational Frequencies J. Comput. Chem. 1996, 17, 553-586 (Pubitemid 126567069)
25. Halgren, T. A.; Nachbar, R. B. Merck Molecular Force Field. IV. Conformational Energies and Geometries for MMFF94 J. Comput. Chem. 1996, 17, 587-615 (Pubitemid 126567070)
26. Halgren, T. A. Merck Molecular Force Field. V. Extension of MMFF94 Using Experimental Data, Additional Computational Data and Empirical Rules J. Comput. Chem. 1996, 17, 616-641
27. Halgren, T. A. MMFF VI. MMFF94s Option for Energy Minimization Studies J. Comput. Chem. 1999, 20, 720-729
28. Halgren, T. A. MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-Interaction Energies and Geometries J. Comput. Chem. 1999, 20, 730-748
29. Broyden, C. G. The convergence of a class of double-rank minimization algorithms:1. General considerations J. Inst. Math. Appl. 1970, 6, 76-90
30. Fletcher, R. A new approach to variable metric methods Comput. J. 1970, 13, 317-322
31. Goldfarb, D. A family of variable-metric methods derived by variational means Math. Comp. 1970, 24, 23-26
32. Shanno, D. F. Conditioning of quasi-Newton methods for function minimization Math. Comp. 1970, 24, 647-656
33. MOE 2008.10; Chemical Computing Group, Inc.: Montreal, Canada, 2008.
34. Wichapong, K.; Lindner, M.; Pianwanit, S.; Kokpol, S.; Sippl, W. Receptor-based 3D-QSAR studies of checkpoint Wee1 kinase inhibitors Eur. J. Med. Chem. 2009, 44, 1383-1395
35. Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J. Mol. Biol. 1995, 245, 43-53
36. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267, 727-748 (Pubitemid 27170693)
37. Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation J. Comput. Chem. 2002, 23, 1623-1641 (Pubitemid 35330860)
38. Wang, J.; Cieplak, P.; Kollman, P. A. How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules J. Comput. Chem. 2000, 21, 1049-1074
39. Case, D. A.; Darden, T. A.; Cheatham, I. T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California, San Francisco., 2008.
40. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
41. Luo, R.; David, L.; Gilson, M. K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems J. Comput. Chem. 2002, 23, 1244-1253 (Pubitemid 35009216)
42. Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models J. Phys. Chem. 1994, 98, 1978-1988
43. Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction J. Comput.-Aided Mol. Des. 2002, 16, 11-26 (Pubitemid 34855041)
44. Pearlman, D. A.; Charifson, P. S. Improved scoring of ligand-protein interactions using OWFEG free energy grids J. Med. Chem. 2001, 44, 502-511
45. Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking J. Med. Chem. 2006, 49, 6789-67801 (Pubitemid 44749746)